AMBER Archive (2004)

Subject: AMBER: MD with NTR + NMROPT

From: Martin Fabani (Martin.Fabani_at_man.ac.uk)
Date: Mon May 10 2004 - 03:56:28 CDT

Dear AMBER users:
Hi, I'm trying to perform a short MD in AMBER7 and I
would like to know if it is possible to do such simulation
holding a part of my structure fixed (ntr=1) and including
NMR distance restraints (nmropt=1) for another part of
the structure, at the same time. I tried different input
protocols including both requirements but it doesn't
seem to work. Either maintains part of the structure rigid
(and doesn't read the nmr distance restraints) or read
the NMR distance restraints but doesn't keep the other
bit of the molecule fixed.
The typical protocol I used is:
 &cntrl
  igb = 1,
  ntb = 0,
  ntp = 0,
  ntt = 1,
  temp0 = 300.0,
  tempi = 0.0,
  nstlim = 20000,
  dt = 0.001,
  ntwx = 500,
  ntwv = 500,
  ntpr = 500,
  ntwe = 500,
  imin = 0,
  cut = 99.0,
  ntr = 1,
  nmropt = 1,
  saltcon = 0.2,
  gbsa = 1,
 &end
Group input for restrained atoms
 5.0
RES 3 42
END
END
  &wt type = 'END'
 &end
 DISANG = phn.disang
END

In the case I use this protocol the MD will be done only
reading the NMR restraints but NOT keeping part of my
molecule fixed (like it is not reading ntr=1...)

Any ideas??

Thanks a lot
Martin
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